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Question: Bioconductor: quantile normalization
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gravatar for KVC_bioinfo
7 months ago by
KVC_bioinfo0 wrote:

Hello All,

I have used Bioconductor ‘preprocessCore’ fro quantile normalization. I am trying t understand how does it work with low expressed or zero count genes. Is someone aware of that? Does it remove the low expressed genes?

TIA

 

 

ADD COMMENTlink modified 7 months ago by James W. MacDonald48k • written 7 months ago by KVC_bioinfo0
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gravatar for James W. MacDonald
7 months ago by
United States
James W. MacDonald48k wrote:

No, it doesn't remove anything. It wouldn't make any sense to do that. If you look at the help page for normalize.quantiles, there is a link to a pdf that explains the procedure.

That said, preprocessCore, and normalize.quantiles are intended for microarray measurements, and using for count data is probably suboptimal.

ADD COMMENTlink written 7 months ago by James W. MacDonald48k

Thank you very much. I have used that on RNA-seq counts 

ADD REPLYlink written 7 months ago by KVC_bioinfo0

Well, like I said, that is probably not what you want to do. There are established RNA-Seq analysis pipelines, such as DESeq2 and edgeR, which handle the normalization of the count data in a statistically defensible manner. Unless you know what you are doing, it's probably best to use existing tools rather than a hodgepodge of methods borrowed from various analysis pipelines.

ADD REPLYlink written 7 months ago by James W. MacDonald48k
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